In fact there is a way to do this, you will have edit the persistent.sfs file though. What you do is you create a new vessel with a new mechjeb2 part and put it on the landing pad. Than you open the persistent.sfs file from your save's folder in a simple text editor and look for your new vessel's name, somewhere in the vessel's parts tree will be the new mechejeb2 part. When you've found it you open up the file once more in a new editor window and look for the part you want to replace. Now remove all of the old part's values that do not appear in the new part and copy the new ones to the old part, also change the edited part's name to "mumech.MJ2.AR202". Don't forget to back-up all files in question before you start editing. I hope this works for you, it did for me.